I don't believe you can, actually. Migration Assistant (which is also run post-install) shows you categories of information you'd like to transfer, but strangely, Applications is just a single category. I assume that the configuration data for your applications would be covered elsewhere, regardless. So I generally take the view that migrations should be all or nothing: either rely on it to completely restore your system, or don't use it at all and manually copy the data and apps you want out of your backups.
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